Receptor
PDB id Resolution Class Description Source Keywords
3BXF 1.7 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF EFFECTOR BINDING DOMAIN OF CENTRAL GLYC GENE REGULATOR (CGGR) FROM BACILLUS SUBTILIS IN COMPLEX WITF RUCTOSE-1,6-BISPHOSPHATE BACILLUS SUBTILIS EFFECTOR BINDING DOMAIN CATABOLIC REPRESSOR TRANSCRIPTIONAREGULATOR DEOR FAMILY DNA-BINDING TRANSCRIPTION REGULATIREGULATION
Ref.: CRYSTAL STRUCTURES OF THE EFFECTOR-BINDING DOMAIN O REPRESSOR CENTRAL GLYCOLYTIC GENE REGULATOR FROM BA SUBTILIS REVEAL LIGAND-INDUCED STRUCTURAL CHANGES U BINDING OF SEVERAL GLYCOLYTIC INTERMEDIATES. MOL.MICROBIOL. V. 69 895 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
13P B:401;
Valid;
none;
Kd = 3.34 uM
170.058 C3 H7 O6 P C(C(=...
CL B:501;
B:502;
B:503;
B:504;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
FBP A:401;
Valid;
none;
Kd = 2.87 uM
340.116 C6 H14 O12 P2 C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3BXF 1.7 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF EFFECTOR BINDING DOMAIN OF CENTRAL GLYC GENE REGULATOR (CGGR) FROM BACILLUS SUBTILIS IN COMPLEX WITF RUCTOSE-1,6-BISPHOSPHATE BACILLUS SUBTILIS EFFECTOR BINDING DOMAIN CATABOLIC REPRESSOR TRANSCRIPTIONAREGULATOR DEOR FAMILY DNA-BINDING TRANSCRIPTION REGULATIREGULATION
Ref.: CRYSTAL STRUCTURES OF THE EFFECTOR-BINDING DOMAIN O REPRESSOR CENTRAL GLYCOLYTIC GENE REGULATOR FROM BA SUBTILIS REVEAL LIGAND-INDUCED STRUCTURAL CHANGES U BINDING OF SEVERAL GLYCOLYTIC INTERMEDIATES. MOL.MICROBIOL. V. 69 895 2008
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 257 families.
1 3BXG Kd = 10.98 uM BG6 C6 H13 O9 P C([C@@H]1[....
2 3BXF Kd = 3.34 uM 13P C3 H7 O6 P C(C(=O)COP....
3 3BXH Kd = 94.34 uM F6P C6 H13 O9 P C([C@@H]1[....
4 3BXE Kd = 3.34 uM 13P C3 H7 O6 P C(C(=O)COP....
5 2OKG Kd = 63.29 uM G3H C3 H7 O6 P C([C@H](C=....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 3BXG Kd = 10.98 uM BG6 C6 H13 O9 P C([C@@H]1[....
2 3BXF Kd = 3.34 uM 13P C3 H7 O6 P C(C(=O)COP....
3 3BXH Kd = 94.34 uM F6P C6 H13 O9 P C([C@@H]1[....
4 3BXE Kd = 3.34 uM 13P C3 H7 O6 P C(C(=O)COP....
5 2OKG Kd = 63.29 uM G3H C3 H7 O6 P C([C@H](C=....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 185 families.
1 3BXG Kd = 10.98 uM BG6 C6 H13 O9 P C([C@@H]1[....
2 3BXF Kd = 3.34 uM 13P C3 H7 O6 P C(C(=O)COP....
3 3BXH Kd = 94.34 uM F6P C6 H13 O9 P C([C@@H]1[....
4 3BXE Kd = 3.34 uM 13P C3 H7 O6 P C(C(=O)COP....
5 2OKG Kd = 63.29 uM G3H C3 H7 O6 P C([C@H](C=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 13P; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 13P 1 1
2 PGA 0.5 0.818182
3 HPV 0.4375 0.90625
4 PGH 0.424242 0.622222
5 IBS 0.404255 0.815789
Ligand no: 2; Ligand: FBP; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 FBP 1 1
2 AFP 1 1
3 F1X 0.744186 0.954545
4 TA6 0.666667 0.954545
5 F6P 0.666667 0.954545
6 FDP 0.462963 0.954545
7 OI7 0.448276 0.976744
8 F1P 0.418182 0.847826
9 AHG 0.404255 0.930233
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3BXF; Ligand: 13P; Similar sites found: 62
This union binding pocket(no: 1) in the query (biounit: 3bxf.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4KJU 1RH 0.007854 0.42829 None
2 4CUB GAL NAG 0.007436 0.41992 None
3 3ENV ABF 0.008122 0.4101 1.2766
4 5IDB MAN 0.02561 0.40142 1.40845
5 5IDB BMA 0.02561 0.40142 1.40845
6 1FS5 TLA 0.0001191 0.48418 1.96078
7 2G30 ALA ALA PHE 0.001198 0.45493 2.7451
8 2B6N ALA PRO THR 0.006749 0.42892 2.7451
9 5EB4 FAD 0.00778 0.42823 2.7451
10 1MXG ACR 0.01514 0.40542 2.7451
11 1X9Q FLU 0.01759 0.40219 2.7451
12 4CCW VKC 0.01627 0.40099 2.7451
13 1SW0 PGA 0.003669 0.42626 2.82258
14 2Z49 AMG 0.002564 0.43571 3.13725
15 2D24 XYS XYS 0.01055 0.41033 3.13725
16 1TRD PGH 0.006665 0.41412 3.2
17 3EB9 FLC 0.00007623 0.50491 3.52941
18 3WSG CIT 0.01477 0.41039 3.57143
19 1KSK URA 0.006372 0.4354 3.84615
20 1O8B ABF 0.0003335 0.487 3.92157
21 3BJE URA 0.0103 0.42557 3.92157
22 5MZN ADP 0.02345 0.40016 3.92157
23 4DSU BZI 0.01484 0.41352 4.2328
24 5KJW 53C 0.008651 0.42768 4.31373
25 4N8I COA 0.005714 0.41768 4.31373
26 3UOY NAP 0.03523 0.41325 4.70588
27 1VBO MAN 0.01825 0.40105 4.70588
28 2DUR MAN MAN 0.0105 0.42551 4.74308
29 1QDS PGA 0.006489 0.41899 4.78088
30 2DBX GLU 0.0146 0.41101 5.09804
31 1VL1 CIT 0.000001741 0.62184 5.17241
32 2UVO NAG 0.01345 0.41125 5.26316
33 3N9R TD3 0.005429 0.42271 5.4902
34 4NZ6 DGL 0.009647 0.42135 5.4902
35 5HWV MBN 0.01471 0.41048 5.4902
36 3G1Z AMP 0.01064 0.40866 5.4902
37 4F8L AES 0.02921 0.40017 5.51724
38 2WZ5 MET 0.005745 0.4371 6.53595
39 4WCX MET 0.005267 0.42748 6.66667
40 1VR0 3SL 0.007635 0.42011 6.66667
41 1I1E DM2 0.01322 0.41283 6.66667
42 2C3H GLC GLC 0.008848 0.41576 7.14286
43 1M0S CIT 0.001455 0.45555 7.30594
44 2YVF FAD 0.02786 0.41491 7.45098
45 5CIC 51R 0.02075 0.40249 7.84314
46 1LK7 DER 0.0006099 0.46271 7.86026
47 1UJ5 5RP 0.0003461 0.4742 7.92952
48 1SC3 MLI 0.00774 0.42688 8.42697
49 4MIG G3F 0.01906 0.41625 8.62745
50 2YPI PGA 0.003775 0.43028 8.90688
51 3FIU POP 0.02087 0.40171 9.23695
52 3QPB URA 0.01469 0.41589 9.80392
53 3OQJ 3CX 0.009764 0.41046 9.80392
54 2RI1 GLP 0.000004497 0.45993 10.6383
55 2BKX F6R 0.00005903 0.50376 10.7438
56 5F6U 5VK 0.01617 0.40478 10.828
57 1WOQ BGC 0.009436 0.41117 10.9804
58 1NE7 AGP 0.0001164 0.49032 12.9412
59 2Y69 CHD 0.01835 0.40897 15
60 5TCI MLI 0.02917 0.40349 16.4706
61 5BWD FUM 0.01474 0.41239 18.8235
62 5MRH Q9Z 0.009087 0.41638 22.3529
Pocket No.: 2; Query (leader) PDB : 3BXF; Ligand: FBP; Similar sites found: 44
This union binding pocket(no: 2) in the query (biounit: 3bxf.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4KJU 1RH 0.007145 0.43568 None
2 3ENV ABF 0.008792 0.41225 1.2766
3 1FS5 TLA 0.00007821 0.49722 1.96078
4 1P77 ATR 0.01311 0.41668 2.35294
5 2G30 ALA ALA PHE 0.0008319 0.48545 2.7451
6 2B6N ALA PRO THR 0.009625 0.42292 2.7451
7 4ZBY URA 0.0266 0.40406 3.09278
8 4LO2 GAL BGC 0.02107 0.40037 3.13725
9 3EB9 FLC 0.00003843 0.52387 3.52941
10 5LY1 PPI 0.01433 0.40594 3.52941
11 1O8B ABF 0.0002412 0.49854 3.92157
12 3BJE URA 0.01356 0.42225 3.92157
13 4DSU BZI 0.01951 0.41033 4.2328
14 5KJW 53C 0.01375 0.4217 4.31373
15 4OUJ LBT 0.01461 0.40569 4.31373
16 4N8I COA 0.007499 0.40564 4.31373
17 3ZJX BOG 0.02671 0.40181 4.31373
18 4URX HXY 0.01728 0.42062 4.32432
19 1VBO MAN 0.01267 0.41668 4.70588
20 5FPE 3TR 0.03147 0.40794 4.70588
21 3PLN U5P 0.02563 0.4017 4.70588
22 1VL1 CIT 0.000004496 0.60522 5.17241
23 3G1Z AMP 0.004145 0.43228 5.4902
24 3N9R TD3 0.01081 0.41204 5.4902
25 2I4O ATP 0.01495 0.40518 5.4902
26 2EB5 OXL 0.02878 0.40029 5.61798
27 4WCX MET 0.006303 0.42857 6.66667
28 1I1E DM2 0.01897 0.40844 6.66667
29 1M0S CIT 0.001332 0.46166 7.30594
30 1LK7 DER 0.0007881 0.46185 7.86026
31 1UJ5 5RP 0.0004192 0.47481 7.92952
32 1SC3 MLI 0.01144 0.41969 8.42697
33 5DYO FLU 0.02895 0.40365 9.43396
34 4IF4 BEF 0.02021 0.41242 9.61539
35 4MOB ADP 0.009095 0.42721 9.80392
36 3QPB URA 0.02338 0.40922 9.80392
37 3OQJ 3CX 0.01571 0.40413 9.80392
38 2RI1 GLP 0.000004087 0.44083 10.6383
39 2BKX F6R 0.00003146 0.52134 10.7438
40 5F6U 5VK 0.02295 0.40761 10.828
41 1NE7 AGP 0.00006854 0.50573 12.9412
42 5TCI MLI 0.03122 0.40548 16.4706
43 5MRH Q9Z 0.002931 0.44462 22.3529
44 1MO9 KPC 0.04927 0.40609 22.3529
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